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G/meskel W, Desta K, Diriba R, Belachew M, Evans M, Cantarelli V, Urrego M, Sisay A, Gebreegziabxier A, Abera A. SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction-based assays in Addis Ababa, Ethiopia. IJID Reg 2024; 11:100363. [PMID: 38634071 PMCID: PMC11021353 DOI: 10.1016/j.ijregi.2024.100363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024]
Abstract
Objectives This study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)-based variant detection in Addis Ababa, Ethiopia. Methods A cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 μl RNA and 20 μl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive. Results A total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30. Conclusions The study data demonstrated that reverse transcription-PCR-based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.
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Affiliation(s)
- Wodneh G/meskel
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Kassu Desta
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Regasa Diriba
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Mahlet Belachew
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Martin Evans
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Vlademir Cantarelli
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Maritza Urrego
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | | | - Adugna Abera
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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Hazim C, Abubeker Ibrahim R, Westercamp M, Belete GA, Amare Kibret B, Kanter T, Yimer G, Adem TS, Stevenson KB, Urrego M, Kale KN, Omondi MW, VanderEnde D, Park BJ, Parsons MMB, Gallagher KM. Establishment of a Sentinel Laboratory-Based Antimicrobial Resistance Surveillance Network in Ethiopia. Health Secur 2019; 16:S30-S36. [PMID: 30480505 DOI: 10.1089/hs.2018.0052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In 2014, as part of the Global Health Security Agenda, Ethiopia was provided the technical and financial resources needed to prioritize antimicrobial resistance (AMR) in the national public health sphere. Under the direction of a multi-stakeholder working group, AMR surveillance was launched in July 2017 at 4 sentinel sites across the country. The AMR surveillance initiative in Ethiopia represents one of the first systematic efforts to prospectively collect, analyze, and report national-level microbiology results from a network of hospitals and public health laboratories in the country. Baseline readiness assessments were conducted to identify potential challenges to implementation to be addressed through capacity-building efforts. As part of these efforts, the working group leveraged existing resources, initiated laboratory capacity building through mentorship, and established infrastructure and systems for quality assurance, data management, and improved coordination. As a result, AMR surveillance data are being reported and analyzed for use; data from more than 1,700 patients were collected between July 2017 and March 2018. The critical challenges and effective solutions identified through surveillance planning and implementation have provided lessons to help guide successful AMR surveillance in other settings. Ultimately, the surveillance infrastructure, laboratory expertise, and communication frameworks built specifically for AMR surveillance in Ethiopia can be extended for use with other infectious diseases and potential public health emergencies. Thus, building AMR surveillance in Ethiopia has illustrated how laying the foundation for a specific public health initiative can develop capacity for core public health functions with potential benefit.
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Affiliation(s)
- Carmen Hazim
- Carmen Hazim, MPH, is an Epidemiologist, the Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Rajiha Abubeker Ibrahim
- Rajiha Abubeker Ibrahim, MSc, is a Researcher, Clinical Bacteriology and Mycology Research Team, the Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Matthew Westercamp
- Matthew Westercamp, PhD, is an Epidemiologist, the Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Gebrie Alebachew Belete
- Gebrie Alebachew Belete, MSc, is AMR Coordinator, Bacteriology, Parasitology, and Zoonosis Directorate, the Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Berhanu Amare Kibret
- Berhanu Amare Kibret, MD, MPH, MBA, is Global Health Security-Technical Officer, the Division of Global Health Protection, CDC, Addis Ababa, Ethiopia
| | - Theresa Kanter
- Theresa Kanter, MURP, is Program Deputy, the Division of Global Health Protection, CDC, Addis Ababa, Ethiopia
| | - Getnet Yimer
- Getnet Yimer, PhD, is East Africa Regional Director, Global One Health Initiative, Ohio State University, Addis Ababa, Ethiopia
| | - Thuria Siraj Adem
- Thuria Siraj Adem, MPH, is ASM Local Consultant for Ethiopia, International Affairs, American Society for Microbiology (ASM), Addis Ababa, Ethiopia
| | - Kurt B Stevenson
- Kurt B. Stevenson, MD, is Professor of Medicine and Epidemiology, Department of Internal Medicine, College of Medicine, Ohio State University, Columbus, Ohio
| | - Maritza Urrego
- Maritza Urrego, BBA, CPM, is Program Specialist, International Affairs, ASM, Washington, DC
| | - Kashmira N Kale
- Kashmira N. Kale, MPH, MBA, is PHI/CDC Global Health Fellow, the Division of Global Health Protection, CDC, Addis Ababa, Ethiopia
| | - Michael W Omondi
- Michael W. Omondi, MS, is a Microbiologist, the Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Daniel VanderEnde
- Daniel VanderEnde, MD, is Medical Officer, the Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Benjamin J Park
- Benjamin J. Park, MD, is Chief, International Infection Control Program, the Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Michele M B Parsons
- Michele M. B. Parsons, PhD, is a Microbiologist, Center for Global Health, Division of Global Health Protection, CDC, Atlanta
| | - Kathleen M Gallagher
- Kathleen M. Gallagher, DSc, is Program Director, the Division of Global Health Protection, CDC, Addis Ababa, Ethiopia
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Baldwin MK, Alvarez C, Rincon M, Quintero A, Urrego M, Guerra C, Edna F, Taborda N, Hersh AR, Muñoz LF, Moreno DJ, Rubio ML, Vargas JC, Tolosa JE. An implementation strategy to increase uptake of immediate postpartum contraception: the COMSE trial. Contraception 2017. [DOI: 10.1016/j.contraception.2017.07.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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